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1.
Virus Evol ; 8(1): veac005, 2022.
Article in English | MEDLINE | ID: covidwho-1874000

ABSTRACT

Influenza type-A viruses (IAVs) present a global burden of human respiratory infections and mortality. Genome reassortment is an important mechanism through which epidemiologically novel influenza viruses emerge and a core step in the safe reassortment-incompetent live-attenuated influenza vaccine development. Currently, there are no data on the rate, spatial and temporal distribution, and role of reassortment in the evolution and diversification of IAVs circulating in Africa. We aimed to detect intra-subtype reassortment among Africa pandemic H1N1pdm09 (2009-10), seasonal H1N1pdm09 (2011-20), and seasonal H3N2 viruses and characterize the genomic architecture and temporal and spatial distribution patterns of the resulting reassortants. Our study was nested within the Uganda National Influenza Surveillance Programme. Next-generation sequencing was used to generate whole genomes (WGs) from 234 H1N1pdm09 (n = 116) and H3N2 (n = 118) viruses sampled between 2010 and 2018 from seven districts in Uganda. We combined our newly generated WGs with 658 H1N1pdm09 and 1131 H3N2 WGs sampled between 1994 and 2020 across Africa and identified reassortants using an automated Graph Incompatibility Based Reassortment Finder software. Viral reassortment rates were estimated using a coalescent reassortant constant population model. Phylogenetic analysis was used to assess the effect of reassortment on viral genetic evolution. We observed a high frequency of intra-subtype reassortment events, 12 · 4 per cent (94/758) and 20 · 9 per cent (256/1,224), and reassortants, 13 · 3 per cent (101/758) and 38 · 6 per cent (472/1,224), among Africa H1N1pdm09 and H3N2 viruses, respectively. H1N1pdm09 reassorted at higher rates (0.1237-0.4255) than H3N2 viruses (0 · 00912-0.0355 events/lineage/year), a case unique to Uganda. Viral reassortants were sampled in 2009 through 2020, except in 2012. 78 · 2 per cent (79/101) of H1N1pdm09 reassortants acquired new non-structural, while 57 · 8 per cent (273/472) of the H3N2 reassortants had new hemagglutinin (H3) genes. Africa H3N2 viruses underwent more reassortment events involving larger reassortant sets than H1N1pdm09 viruses. Viruses with a specific reassortment architecture circulated for up to five consecutive years in specific countries and regions. The Eastern (Uganda and Kenya) and Western Africa harboured 84 · 2 per cent (85/101) and 55 · 9 per cent (264/472) of the continent's H1N1pdm09 and H3N2 reassortants, respectively. The frequent reassortment involving multi-genes observed among Africa IAVs showed the intracontinental viral evolution and diversification possibly sustained by viral importation from outside Africa and/or local viral genomic mixing and transmission. Novel reassortant viruses emerged every year, and some persisted in different countries and regions, thereby presenting a risk of influenza outbreaks in Africa. Our findings highlight Africa as part of the global influenza ecology and the advantage of implementing routine whole-over partial genome sequencing and analyses to monitor circulating and detect emerging viruses. Furthermore, this study provides evidence and heightens our knowledge on IAV evolution, which is integral in directing vaccine strain selection and the update of master donor viruses used in recombinant vaccine development.

2.
J R Soc Interface ; 18(185): 20210608, 2021 12.
Article in English | MEDLINE | ID: covidwho-1865053

ABSTRACT

Due to its high lethality among older people, the safety of nursing homes has been of central importance during the COVID-19 pandemic. With test procedures and vaccines becoming available at scale, nursing homes might relax prohibitory measures while controlling the spread of infections. By control we mean that each index case infects less than one other person on average. Here, we develop an agent-based epidemiological model for the spread of SARS-CoV-2 calibrated to Austrian nursing homes to identify optimal prevention strategies. We find that the effectiveness of mitigation testing depends critically on test turnover time (time until test result), the detection threshold of tests and mitigation testing frequencies. Under realistic conditions and in absence of vaccinations, we find that mitigation testing of employees only might be sufficient to control outbreaks if tests have low turnover times and detection thresholds. If vaccines that are 60% effective against high viral load and transmission are available, control is achieved if 80% or more of the residents are vaccinated, even without mitigation testing and if residents are allowed to have visitors. Since these results strongly depend on vaccine efficacy against infection, retention of testing infrastructures, regular testing and sequencing of virus genomes is advised to enable early identification of new variants of concern.


Subject(s)
COVID-19 , Pandemics , Aged , Humans , Nursing Homes , SARS-CoV-2 , Vaccination
4.
Arthritis Rheumatol ; 74(5): 909-910, 2022 May.
Article in English | MEDLINE | ID: covidwho-1849987
5.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-333072

ABSTRACT

Objectives: To investigate the intensity and longevity of SARS-CoV-2 vaccination response in patients with immune-mediated inflammatory disease (IMID) by diagnosis, treatment and adapted vaccination schedules. Methods SARS-CoV-2 IgG antibody response after SARS-CoV-2 vaccination was measured longitudinally in a large prospective cohort of healthy controls (HC) and IMID patients between December 2020 and 2021. Demographic and disease-specific data were recorded. Humoral response was compared across treatment and disease groups, and with respect to receipt of booster vaccinations. Age and sex adjusted SARS-CoV-2 antibody response was modelled over time. Marginal mean antibody levels and marginal risks of poor response were calculated at weekly intervals starting from week-8 after the first vaccination up to week 40. Results Among 5076 individuals registered, 2535 IMID patients and 1198 HC were eligible for this analysis. Mean antibody levels were higher in HC compared to IMIDs at all-time points, with peak antibody response in HC more than twice that in IMIDs (12.48 (11.52-13.52) vs. 5.71 (5.46-5.97)). Poor response to vaccination was observed in IMID patients treated with agents affecting B- and T-cell functions. Mean differences in antibody response between IMID diseases were small. After additional vaccinations, IMID patients could achieve higher antibody levels than HC vaccinated according to the two-dose schedule, even-though initial antibody levels were lower. Conclusions IMID patients show a lower and less durable SARS-CoV-2 vaccination response and are at risk to lose humoral immune protection. Adjusted vaccination schedules with earlier boosters and/or more frequent re-doses could better protect IMID patients.

6.
Frontiers in digital health ; 4, 2022.
Article in English | EuropePMC | ID: covidwho-1781955

ABSTRACT

The specification and application of policies and guidelines for public health, medical education and training, and screening programmes for preventative medicine are all predicated on trust relationships between medical authorities, health practitioners and patients. These relationships are in turn predicated on a verbal contract that is over two thousand years old. The impact of information and communication technology (ICT), underpinning Health 4.0, has the potential to disrupt this analog relationship in several dimensions;but it also presents an opportunity to strengthen it, and so to increase the take-up and effectiveness of new policies. This paper develops an analytic framework for the trust relationships in Health 4.0, and through three use cases, assesses a medical policy, the introduction of a new technology, and the implications of that technology for the trust relationships. We integrate this assessment in a set of actionable recommendations, in particular that the trust framework should be part of the design methodology for developing and deploying medical applications. In a concluding discussion, we advocate that, in a post-pandemic world, IT to support policies and programmes to address widespread socio-medical problems with mental health, long Covid, physical inactivity and vaccine misinformation will be essential, and for that, strong trust relationships between all the stakeholders are absolutely critical.

7.
Viruses ; 14(3)2022 03 21.
Article in English | MEDLINE | ID: covidwho-1753693

ABSTRACT

Only limited data are available regarding the immunogenicity of the BNT162b2 mRNA vaccine in HIV-1+ patients. Therefore, we investigated the humoral immune response after BNT162b2-mRNA vaccination or SARS-CoV-2 infection in HIV-1+ patients on antiretroviral therapy compared to HIV-1-uninfected subjects. Serum and saliva samples were analysed by SARS-CoV-2 spike-specific IgG and IgA ELISAs and a surrogate neutralization assay. While all subjects developed anti-spike IgG and IgA and neutralizing antibodies in serum after two doses of BNT162b2 mRNA vaccine, the HIV-1+ subjects displayed significantly lower neutralizing capacity and anti-spike IgA in serum compared to HIV-1-uninfected subjects. Serum levels of anti-spike IgG and neutralizing activity were significantly higher in vaccinees compared to SARS-CoV-2 convalescents irrespective of HIV-1 status. Among SARS-CoV-2 convalescents, there was no significant difference in spike-specific antibody response between HIV-1+ and uninfected subjects. In saliva, anti-spike IgG and IgA antibodies were detected both in vaccinees and convalescents, albeit at lower frequencies compared to the serum and only rarely with detectable neutralizing activity. In summary, our study demonstrates that the BNT162b2 mRNA vaccine induces SARS-CoV-2-specific antibodies in HIV-1-infected patients on antiretroviral therapy, however, lower vaccine induced neutralization activity indicates a lower functionality of the humoral vaccine response in HIV-1+ patients.


Subject(s)
COVID-19 , HIV-1 , Viral Vaccines , COVID-19/prevention & control , Humans , RNA, Messenger/genetics , SARS-CoV-2 , Vaccination , Vaccines, Synthetic
8.
Clin Chem Lab Med ; 60(6): 941-951, 2022 05 25.
Article in English | MEDLINE | ID: covidwho-1714815

ABSTRACT

OBJECTIVES: The assessment of SARS-CoV-2 infections in children is still challenging, but essential for appropriate political decisions. The aim of this study was to investigate whether residual blood samples can be used for SARS-CoV-2 seroprevalence monitoring in pediatrics. METHODS: In this repeated cross-sectional cohort study, anonymous residual blood samples from pediatric patients aged 0-17 years were collected in three time-periods (Oct.-Nov. 2020, April 2021, and June-July 2021) and analyzed for SARS-CoV-2 Spike protein (anti-S) and nucleocapsid (anti-N) antibodies using commercial antibody assays. 28 reactive samples were used to compare antibody levels with a pseudotyped neutralization assay. The results were further compared to the official national COVID-19 surveillance data to calculate the number of unreported cases. RESULTS: In total, n=2,626 individual blood samples were analyzed. In this unvaccinated pediatric cohort anti-S and anti-N antibody seroprevalence increased over the three time periods (anti-S: 1.38-9.16%, and 14.59%; anti-N: 1.26%, to 6.19%, and 8.56%). Compared to the national surveillance data this leads to a 3.93-5.66-fold increase in the number of unreported cases. However, a correlation between the cumulative incidence of the individual provinces and our assigned data was found (r=0.74, p=0.0151). In addition, reactive samples with anti-S and anti-N and samples with only anti-S showed neutralization capabilities (11/14 and 8/14, respectively). Anti-S levels were not significantly different between age groups and sexes (all p>0.05). CONCLUSIONS: The present study suggests that residual blood samples from routine laboratory chemistry could be included in the estimation of the total SARS-CoV-2 seroprevalence in children.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Viral , COVID-19/diagnosis , COVID-19/epidemiology , Chemistry, Clinical , Child , Cross-Sectional Studies , Humans , Seroepidemiologic Studies , Spike Glycoprotein, Coronavirus
9.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-314898

ABSTRACT

Due to its high lethality amongst the elderly, the safety of nursing homes has been of central importance during the COVID-19 pandemic. With test procedures becoming available at scale, such as antigen or RT-LAMP tests, and increasing availability of vaccinations, nursing homes might be able to safely relax prohibitory measures while controlling the spread of infections (meaning an average of one or less secondary infections per index case). Here, we develop a detailed agent-based epidemiological model for the spread of SARS-CoV-2 in nursing homes to identify optimal prevention strategies. The model is microscopically calibrated to high-resolution data from nursing homes in Austria, including detailed social contact networks and information on past outbreaks. We find that the effectiveness of mitigation testing depends critically on the timespan between test and test result, the detection threshold of the viral load for the test to give a positive result, and the screening frequencies of residents and employees. Under realistic conditions and in absence of an effective vaccine, we find that preventive screening of employees only might be sufficient to control outbreaks in nursing homes, provided that turnover times and detection thresholds of the tests are low enough. If vaccines that are moderately effective against infection and transmission are available, control is achieved if 80% or more of the inhabitants are vaccinated, even if no preventive testing is in place and residents are allowed to have visitors. Since these results strongly depend on vaccine efficacy against infection, retention of testing infrastructures, regular voluntary screening and sequencing of virus genomes is advised to enable early identification of new variants of concern.

10.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-322346

ABSTRACT

Countries around the world implement nonpharmaceutical interventions (NPIs) to mitigate the spread of COVID-19. Design of efficient NPIs requires identification of the structure of the disease transmission network. We here identify the key parameters of the COVID-19 transmission network for time periods before, during, and after the application of strict NPIs for the first wave of COVID-19 infections in Germany combining Bayesian parameter inference with an agent-based epidemiological model. We assume a Watts-Strogatz small-world network which allows to distinguish contacts within clustered cliques and unclustered, random contacts in the population, which have been shown to be crucial in sustaining the epidemic. In contrast to other works, which use coarse-grained network structures from anonymized data, like cell phone data, we consider the contacts of individual agents explicitly. We show that NPIs drastically reduced random contacts in the transmission network, increased network clustering, and resulted in a change from an exponential to a constant regime of newcases. In this regime, the disease spreads like a wave with a finite wave speed that depends on the number of contacts in a nonlinear fashion, which we can predict by mean field theory. Our analysis indicates that besides the well-known transitionbetween exponential increase and exponential decrease in the number of new cases, NPIs can induce a transition to another, previously unappreciated regime of constant new cases.

11.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-321594

ABSTRACT

Immune-mediated inflammatory diseases (IMIDs) of the joints, gut and skin are treated with inhibitors of inflammatory cytokines. These cytokines are involved in the pathogenesis of coronavirus disease 2019 (COVID-19). Investigating anti-SARS-CoV-2 antibody responses in IMIDs we observed a significantly reduced incidence of SARS-CoV-2 infection in IMID patients treated with cytokine inhibitors compared to patients receiving no such inhibitors and two healthy control populations, despite similar social exposure. Hence, cytokine inhibitors seem to at least partially protect from SARS-CoV-2 infection.Authors David Simon and Koray Tascilar contributed equally to this work. Authors Markus F. Neurath and Georg Schett share senior authorship.

12.
Pan Afr Med J ; 40: 185, 2021.
Article in English | MEDLINE | ID: covidwho-1614294

ABSTRACT

INTRODUCTION: we present a qualitative analysis of opinions of the Nigerian general public as to how successful healthcare strategies have been in containing the COVID-19 outbreak. METHODS: an online qualitative survey was conducted, consisting of 30 semi-structured questions. RESULTS: four hundred and ninety-five (495) respondents participated, ranging in age from 18 to 59 years. Over 40% of all respondents were critical of public health information. Participants saw provision of social support measures (n = 83), lack of economic, financial and social support (n = 65), enforcement of restrictions on movement outside the home, availability of face-masks and social distancing (n = 53) and provision of COVID-19 testing (n = 48) as the major things that were handled poorly by the government and health authorities. CONCLUSION: we advocate coordinated forward planning for public safety until vaccines are widely available; while social distancing should continue. Policymakers need to be adaptable to changing conditions, given fluctuating case numbers and fatality rates.


Subject(s)
COVID-19 , Adolescent , Adult , COVID-19 Testing , Humans , Masks , Middle Aged , Nigeria , SARS-CoV-2 , Young Adult
13.
Arthritis Rheumatol ; 74(5): 783-790, 2022 05.
Article in English | MEDLINE | ID: covidwho-1589173

ABSTRACT

OBJECTIVE: To investigate the impact of biologic disease-modifying antirheumatic drug (bDMARD) treatment on the prevalence, seroconversion rate, and longevity of the humoral immune response against SARS-CoV-2 in patients with immune-mediated inflammatory diseases (IMIDs). METHODS: Anti-SARS-CoV-2 IgG antibodies were measured in a prospective cohort of health care professional controls and non-health care controls and IMID patients receiving no treatment or receiving treatment with conventional or biologic DMARDs during the first and second COVID-19 waves. Regression models adjusting for age, sex, sampling time, and exposure risk behavior were used to calculate relative risks (RRs) of seropositivity. Seroconversion rates were assessed in participants with polymerase chain reaction (PCR)-positive SARS-CoV-2 infection. Antibody response longevity was evaluated by reassessing participants who tested positive during the first wave. RESULTS: In this study, 4,508 participants (2,869 IMID patients and 1,639 controls) were analyzed. The unadjusted RR (0.44 [95% confidence interval (95% CI) 0.31-0.62]) and adjusted RR (0.50 [95% CI 0.34-0.73]) for SARS-CoV-2 IgG antibodies were significantly lower in IMID patients treated with bDMARDs compared to non-health care controls (P < 0.001), primarily driven by treatment with tumor necrosis factor inhibitors, interleukin-17 (IL-17) inhibitors, and IL-23 inhibitors. Adjusted RRs for untreated IMID patients (1.12 [95% CI 0.75-1.67]) and IMID patients receiving conventional synthetic DMARDs (0.70 [95% CI 0.45-1.08]) were not significantly different from non-health care controls. Lack of seroconversion in PCR-positive participants was more common among bDMARD-treated patients (38.7%) than in non-health care controls (16%). Overall, 44% of positive participants lost SARS-CoV-2 antibodies by follow-up, with higher rates in IMID patients treated with bDMARDs (RR 2.86 [95% CI 1.43-5.74]). CONCLUSION: IMID patients treated with bDMARDs have a lower prevalence of SARS-CoV-2 antibodies, seroconvert less frequently after SARS-CoV-2 infection, and may exhibit a reduced longevity of their humoral immune response.


Subject(s)
Antirheumatic Agents , Biological Products , COVID-19 , Antibodies, Viral , Antirheumatic Agents/therapeutic use , Cytokines , Humans , Immunity, Humoral , Immunoglobulin G , Prevalence , Prospective Studies , SARS-CoV-2 , Seroconversion
14.
Ann Rheum Dis ; 2021 Nov 24.
Article in English | MEDLINE | ID: covidwho-1532998

ABSTRACT

OBJECTIVES: To test whether patients with immune-mediated inflammatory disease (IMIDs), who did not respond to two doses of the SARS-CoV-2 vaccine, develop protective immunity, if a third vaccine dose is administered. METHODS: Patients with IMID who failed to seroconvert after two doses of SARS-CoV-2 vaccine were subjected to a third vaccination with either mRNA or vector-based vaccines. Anti-SARS-CoV-2 IgG, neutralising activity and T cell responses were assessed at baseline and 3 weeks after revaccination and also evaluated seprarately in rituximab (RTX) and non-RTX exposed patients. RESULTS: 66 non-responders were recruited, 33 treated with RTX, and 33 non-exposed to RTX. Overall, 49.2% patients seroconverted and 50.0% developed neutralising antibody activity. Seroconversion (78.8% vs 18.2%) and neutralising activity (80.0% vs 21.9%) was higher in non-RTX than RTX-treated patients with IMID, respectively. Humoral vaccination responses were not different among patients showing positive (59.3%) or negative (49.7%) T cell responses at baseline. Patients remaining on mRNA-based vaccines showed similar vaccination responses compared with those switching to vector-based vaccines. CONCLUSIONS: Overall, these data strongly argue in favor of a third vaccination in patients with IMID lacking response to standard vaccination irrespective of their B cell status.

15.
Arthritis Rheumatol ; 74(1): 33-37, 2022 01.
Article in English | MEDLINE | ID: covidwho-1527417

ABSTRACT

OBJECTIVE: B cell depletion is an established therapeutic principle in a wide range of autoimmune diseases. However, B cells are also critical for inducing protective immunity after infection and vaccination. We undertook this study to assess humoral and cellular immune responses after infection with or vaccination against SARS-CoV-2 in patients with B cell depletion and controls who are B cell-competent. METHODS: Antibody responses (tested using enzyme-linked immunosorbent assay) and T cell responses (tested using interferon-γ enzyme-linked immunospot assay) against the SARS-CoV-2 spike S1 and nucleocapsid proteins were assessed in a limited number of previously infected (n = 6) and vaccinated (n = 8) autoimmune disease patients with B cell depletion, as well as previously infected (n = 30) and vaccinated (n = 30) healthy controls. RESULTS: As expected, B cell and T cell responses to the nucleocapsid protein were observed only after infection, while respective responses to SARS-CoV-2 spike S1 were found after both infection and vaccination. A SARS-CoV-2 antibody response was observed in all vaccinated controls (30 of 30 [100%]) but in none of the vaccinated patients with B cell depletion (0 of 8). In contrast, after SARS-CoV-2 infection, both the patients with B cell depletion (spike S1, 5 of 6 [83%]; nucleocapsid, 3 of 6 [50%]) and healthy controls (spike S1, 28 of 30 [93%]; nucleocapsid, 28 of 30 [93%]) developed antibodies. T cell responses against the spike S1 and nucleocapsid proteins were found in both infected and vaccinated patients with B cell depletion and in the controls. CONCLUSION: These data show that B cell depletion completely blocks humoral but not T cell SARS-CoV-2 vaccination response. Furthermore, limited humoral immune responses are found after SARS-CoV-2 infection in patients with B cell depletion.


Subject(s)
Autoimmune Diseases/immunology , B-Lymphocytes/immunology , COVID-19 Vaccines/immunology , COVID-19/immunology , Lymphocyte Depletion/adverse effects , SARS-CoV-2/immunology , Autoimmune Diseases/drug therapy , Autoimmune Diseases/virology , COVID-19/prevention & control , Humans , Immunity, Cellular/immunology , Immunity, Humoral/immunology
16.
PMC; 2020.
Preprint in English | PMC | ID: ppcovidwho-292082

ABSTRACT

Countries around the world implement nonpharmaceutical interventions (NPIs) to mitigate the spread of COVID-19. Design of efficient NPIs requires identification of the structure of the disease transmission network. We here identify the key parameters of the COVID-19 transmission network for time periods before, during, and after the application of strict NPIs for the first wave of COVID-19 infections in Germany combining Bayesian parameter inference with an agent-based epidemiological model. We assume a Watts–Strogatz small-world network which allows to distinguish contacts within clustered cliques and unclustered, random contacts in the population, which have been shown to be crucial in sustaining the epidemic. In contrast to other works, which use coarse-grained network structures from anonymized data, like cell phone data, we consider the contacts of individual agents explicitly. We show that NPIs drastically reduced random contacts in the transmission network, increased network clustering, and resulted in a previously unappreciated transition from an exponential to a constant regime of new cases. In this regime, the disease spreads like a wave with a finite wave speed that depends on the number of contacts in a nonlinear fashion, which we can predict by mean field theory.

17.
National Bureau of Economic Research Working Paper Series ; No. 28218, 2020.
Article in English | NBER, Grey literature | ID: grc-748391

ABSTRACT

An extensive literature in economics documents large and persistent declines in earnings following involuntary job loss. We study whether the public safety net mitigates this loss in resources using the Survey of Income and Program Participation in 1996-2013. With an individual fixed effects model, we document which public safety net programs provide the most insurance, and how this varies by pre-job-loss characteristics. We find that Unemployment Insurance provides the largest buffer against lost income, but that due to the structure of the program, the neediest are less-well insured (in terms of dollars transferred and percentage of lost earnings replaced), compared to middle and higher income job losers. This has important implications for the progressivity of the safety net, and how best to support displaced workers, which is crucial to understand for job losers at any time, and especially now, in light of the historic number of job losses during the COVID-19 pandemic.

18.
J Law Med Ethics ; 49(3): 415-417, 2021.
Article in English | MEDLINE | ID: covidwho-1492920

ABSTRACT

Telehealth has the potential to address health disparities, but not without deliberate choices about how to implement it. To support vulnerable patients, health policy leaders must pursue creative solutions such as public-private partnerships, broadband infrastructure, and value-based payment. Without these initiatives or others like them, health disparities are likely to persist despite telehealth's tantalizing potential.


Subject(s)
COVID-19 , Telemedicine , Health Policy , Health Services Accessibility , Humans , Public-Private Sector Partnerships
19.
Arthritis Rheumatol ; 74(5): 909-910, 2022 May.
Article in English | MEDLINE | ID: covidwho-1490706
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